AMBER Archive (2004)

Subject: AMBER: xleap don't recognize formaldehyde?

From: scopio (scopio_at_163.com)
Date: Tue Apr 27 2004 - 09:53:00 CDT

Dear Amber Users:

I have a pdb contains a residue called 'FOR'. It consists of only two
atoms which are C atom and O atom. I think 'FOR' stand for formaldehyde.
My problem is that Xleap don't recognize this residue. Could anybody
please give me some clue? Thanks in advance!

Here is the message when xleap load pdb:
==========
Loading PDB file: ./for.pdb
Unknown residue: FOR number: 0 type: Terminal/beginning
..relaxing end constraints to try for a dbase match
   -no luck
Creating new UNIT for residue: FOR sequence: 0
Created a new atom named: C within residue: .R<FOR 0>
Created a new atom named: O within residue: .R<FOR 0>
One sided connection. Residue: missing connect1 atom.
   Added missing heavy atom: .R<CMET 1>.A<OXT 18>
   total atoms in file: 10
   Leap added 10 missing atoms according to residue templates:
        1 Heavy
        9 H / lone pairs
   The file contained 2 atoms not in residue templates
=============

and part of that pdb file
-------
ATOM 7357 C FOR H 0 125.259 43.696 43.028 1.00 37.56
1PRC7521
ATOM 7358 O FOR H 0 124.099 43.291 43.125 1.00 41.65
1PRC7522
ATOM 7359 N MET H 1 125.886 43.318 41.928 1.00 32.03
1PRC7523
ATOM 7360 CA MET H 1 126.906 44.195 41.456 1.00 29.40
1PRC7524
ATOM 7361 C MET H 1 126.733 44.684 40.024 1.00 31.30
1PRC7525
ATOM 7362 O MET H 1 126.671 43.904 39.079 1.00 21.34
1PRC7526
ATOM 7363 CB MET H 1 128.306 43.817 41.904 1.00 28.73
1PRC7527
ATOM 7364 CG MET H 1 128.347 43.483 43.394 1.00 35.23
1PRC7528
ATOM 7365 SD MET H 1 129.882 42.606 43.761 1.00 45.90
1PRC7529
ATOM 7366 CE MET H 1 130.798 43.062 42.257 1.00 35.87
1PRC7530

Best!

Liu

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